Acoustic telemetry migration analysis

Summary

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2014

Timestamp: 2024-07-24 12:39:19.59901

Number of target tags: 40

Number of listed receivers: 7 (of which 0 had no detections)

Data time range: 2014-04-29 01:34:31 to 2014-05-16 20:44:29 (Europe/London).

Percentage of post-release valid detections: 100%

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Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name	Latitude	Longitude	Array	Section	Standard.name	x.29902	y.29902
Layde	55.20140	-6.524300	A1	River	St.1	294010	440363
Sewage works	55.21040	-6.531700	A2	River	St.2	293518	441355
Bushfoot	55.21960	-6.531900	A3	River	St.3	293484	442379
Portballintrae 2	55.22156	-6.541634	A4	Sea	St.4	292860	442584
Portballintrae 3	55.22433	-6.541750	A4	Sea	St.5	292846	442892
Portballintrae 4	55.22632	-6.538917	A4	Sea	St.6	293022	443117
Portballintrae 5	55.22797	-6.536100	A4	Sea	St.7	293197	443304

Deployments

Receiver	Array	Station.name	Standard.name	Start	Stop
102880	A4	Portballintrae 2	St.4	2014-04-29	2015-05-16 23:59:59
102884	A4	Portballintrae 3	St.5	2014-04-29	2015-05-16 23:59:59
102885	A4	Portballintrae 4	St.6	2014-04-29	2015-05-16 23:59:59
102886	A4	Portballintrae 5	St.7	2014-04-29	2015-05-16 23:59:59
107086	A2	Sewage works	St.2	2014-04-29	2015-05-16 23:59:59
107160	A3	Bushfoot	St.3	2014-04-29	2015-05-16 23:59:59
111472	A1	Layde	St.1	2014-04-29	2015-05-16 23:59:59

Release sites

Station.name	Latitude	Longitude	Array	Type	Standard.name	x.29902	y.29902	n.All
Cross	55.10060	-6.405336	A1	Release	Cross	301841	429309	12
Trap	55.20271	-6.523100	A2	Release	Trap	294084	440510	28

Array forward efficiency

Note:

These efficiency calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.

The data used in the tables below is stored in the overall.CJS object. Auxiliary information can also be found in the matrices and arrays objects.

These efficiency values are estimated using the analytical equations provided in the paper “Using mark-recapture models to estimate survival from telemetry data” by Perry et al. (2012). In some situations, more advanced efficiency estimation methods may be required.

You can try running advEfficiency(results$overall.CJS) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Individuals detected and estimated

	A1	A2	A3	A4
detected	10	32	31	28
here plus on peers	10	31	28	-
not here but on peers	1	0	0	-
known	11	32	31	28
estimated	11	32	31	-

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

	A1	A2	A3	A4
efficiency	90.9%	100%	100%	-

Warning messages

Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A4.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.

User comments

No comments were included during the analysis.

Biometric graphics

Note:

The data used in this graphic is the data present in the biometrics.csv file.

Section Survival

Note:

The data used in this table and graphic is stored in the section.overview object.

	Total	Disap..in.River	Migrated.to.Sea	Disap..in.Sea	Succeeded
All	40	9	31	3	28

Last Seen Arrays

Note:

The data used in this graphic is stored in the status.df object (‘Very.last.array’ column).

Progression

Zoom in or open the figure in a new tab to clearly read the text within each circle.

Note:

The progression calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.

The data used in this graphic is stored in the overall.CJS object, and the data used in the tables is stored in the group.overview object. You can find detailed progressions per release site in the release.overview object.

Group: All

	Release	A1	A2	A3	A4
detected	40	10	32	31	28
here plus on peers	-	10	31	28	-
not here but on peers	-	1	0	0	-
known	40	11	32	31	28
estimated	-	11	32	31	-
difference	-	0	0	0	-

Time of arrival at each Array

Note:

Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.

You can replicate these graphics and edit them as needed using the plotTimes() function.

The data used in these graphics is stored in the times object.

To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.

Dotplots

Note:

The top 10% of the values for each panel are marked in red.

The bottom 10% of the values for each panel are marked in blue.

The columns starting with “To” should be read as either “Average time to …” or “Average speed to …”, depending on the unit used. The columns starting with “In” should be read as “Total time in …”. These reductions were made to keep the column headers as short as possible.

The data used in these graphics is stored in the status.df object.

Individual detection plots

Note:

You can choose to plot detections by station or by array using the detections.y.axis argument.

The detections are coloured by section. The vertical black dashed line shows the time of release. The vertical grey dashed lines show the assigned moments of entry and exit for each study area section. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.

Manually edited tag detections are highlighted with yellow graphic borders.

Manually overridden tag detections are highlighted with red graphic borders.

The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.

You can replicate these graphics and edit them as needed using the plotDetections() function.

You can also see the movement events of multiple tags simultaneously using the plotMoves() function.

The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Full log

Actel R package report.
Version: 1.3.0.9007

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2014
Timestamp: 2024-07-24 12:39:19.59901
Function: migration()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: No Code.space column was found in the biometrics. Assigning code spaces based on detections.
M: No 'Group' column found in the biometrics. Assigning all animals to group 'All'.
M: Number of target tags: 40.
M: Matching detections with deployment periods.
M: Number of ALS: 7 (of which 0 had no detections)
M: Data time range: 2014-04-29 01:34:31 to 2014-05-16 20:44:29 (Europe/London).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A4.
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
M: Compiling and checking section movements for the valid tags.
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling migration timetable.
M: Compiling summary information tables.
M: Calculating array efficiency.
M: Saving results as 'actel_migration_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Analysis completed!

-------------------
User interventions:
-------------------
y # save strays?
y # save results?
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Migration function call:
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migration(tz = 'Europe/London', section.order = NULL, datapack = NULL, success.arrays = NULL, max.interval = 60, min.total.detections = 2, min.per.event = c(1, 1), start.time = NULL, stop.time = NULL, speed.method = 'last to first', speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = NULL, inactive.error = NULL, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, if.last.skip.section = TRUE, replicates = NULL, disregard.parallels = TRUE, GUI = 'needed', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Section survival Last seen Progression Arrival times Dotplots Individual detections Full log